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Ignore null values. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@357 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-10 04:18:20 +00:00
parent 2ef2c9e121
commit 56aa98ad30
1 changed files with 7 additions and 6 deletions
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13
java/src/org/broadinstitute/sting/playground/fourbasecaller/CombineSamAndFourProbs.java
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@ -63,13 +63,14 @@ public class CombineSamAndFourProbs extends CommandLineProgram {
String readname = sr.getReadName();
byte[] sq = (byte[]) fourprobMap.get(readname);
if (sr.getReadNegativeStrandFlag()) {
sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
}
sr.setAttribute("SQ", sq);
if (sq != null) {
if (sr.getReadNegativeStrandFlag()) {
sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
}
sw.addAlignment(sr);
sr.setAttribute("SQ", sq);
sw.addAlignment(sr);
}
}
sf.close();